Fix docs and test

.circleci/config.yml

@@ -4,12 +4,39 @@ orbs:
   python: circleci/python@2.1.1
   codecov: codecov/codecov@3.2.2
 
+commands:
+  install_pandoc:
+    description: "Install pandoc"
+    parameters:
+      pandoc_url:
+        type: string
+      pandoc_dest:
+        type: string
+    steps:
+      - restore_cache:
+          keys:
+            - pandoc-download
+      - run:
+          name: Install pandoc
+          command: |
+            if [ ! -f "~/pandoc.tar.gz" ]; then
+              wget << parameters.pandoc_url >> -O ~/pandoc.tar.gz
+            fi
+            sudo tar xvzf ~/pandoc.tar.gz --strip-components 1 -C << parameters.pandoc_dest >>
+      - save_cache:
+          key: pandoc-download
+          paths:
+            - ~/pandoc.tar.gz
+
 jobs:
   build-and-test:
     docker:
       - image: cimg/python:3.8.0
     steps:
       - checkout
+      - restore_cache:
+          keys:
+            - pip-cache
       - run:
           name: Update pip
           command: pip install --upgrade pip
@@ -25,8 +52,46 @@ jobs:
             curl -Os https://uploader.codecov.io/v0.1.0_4653/linux/codecov
             chmod +x codecov
             ./codecov -t ${CODECOV_TOKEN}
+      - save_cache:
+          key: pip-cache
+          paths:
+            - ~/.cache/pip
       - codecov/upload:
           file: coverage.xml
+  build-docs:
+    docker:
+      - image: cimg/python:3.8.0
+    steps:
+      - checkout
+      - restore_cache:
+          keys:
+            - pip-cache-doc
+      - run:
+          name: Update pip
+          command: pip install --upgrade pip
+      - python/install-packages:
+          pkg-manager: pip-dist
+          path-args: .[dev]
+      # Install requirements for docs within docs/requirements.txt
+      - run:
+          name: Install docs requirements
+          command: pip install -r docs/requirements.txt
+      - save_cache:
+          key: pip-cache-doc
+          paths:
+            - ~/.cache/pip
+      - install_pandoc:
+          pandoc_url: "https://github.com/jgm/pandoc/releases/download/2.10/pandoc-2.10-linux-amd64.tar.gz"
+          pandoc_dest: "/usr/local/"
+      - run:
+          name: Build docs
+          no_output_timeout: 20m
+          command: |
+            cd docs
+            make html
+      - store_artifacts:
+          path: docs/_build/html
+          destination: docs
 
   publish:
     docker:
@@ -97,6 +162,10 @@ workflows:
           filters:  # required since `deploy` has tag filters AND requires `build`
             tags:
               only: /.*/
+      - build-docs:
+          filters:  # required since `deploy` has tag filters AND requires `build`
+            tags:
+              only: /.*/
       - publish:
           requires:
             - build-and-test

docs/Makefile

@@ -4,6 +4,7 @@ SPHINXOPTS    = -j auto
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
+# NCORES        ?= $(shell nproc)
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -12,4 +13,4 @@ help:
 .PHONY: help Makefile
 
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) # -j $(NCORES)

docs/_api.rst

@@ -295,10 +295,17 @@ Configuration
 .. automodule:: gpjax.config
 .. currentmodule:: gpjax.config
 
+.. autofunction:: add_parameter
 
-.. autofunction:: get_defaults
+.. autofunction:: get_global_config_if_exists
 
-.. autofunction:: add_parameter
+.. autofunction:: get_default_config
+
+.. autofunction:: update_x64_sensitive_settings
+
+.. autofunction:: get_global_config
+
+.. autofunction:: reset_global_config
 
 
 Quadrature

docs/conf.py

@@ -20,8 +20,6 @@
 
 from importlib_metadata import version
 
-import docs.conf_sphinx_patch
-
 
 def read(*names, **kwargs):
     """Function to decode a read files. Credit GPyTorch."""
@@ -59,7 +57,14 @@ def find_version(*file_paths):
 author = "Thomas Pinder"
 
 # The full version, including alpha/beta/rc tags
-version = find_version("gpjax", "__init__.py")
+import sys
+from os.path import join, pardir, dirname
+
+sys.path.insert(0, join(dirname(__file__), pardir))
+
+import gpjax
+
+version = gpjax.__version__
 release = version
 
 

examples/barycentres.pct.py

@@ -141,7 +141,7 @@ def wasserstein_barycentres(
     cov_stack = jnp.stack(covariances)
     stack_sqrt = jax.vmap(sqrtm)(cov_stack)
 
-    def step(covariance_candidate: jax.Array):
+    def step(covariance_candidate: jax.Array, idx: None):
         inner_term = jax.vmap(sqrtm)(
             jnp.matmul(jnp.matmul(stack_sqrt, covariance_candidate), stack_sqrt)
         )

examples/classification.pct.py

@@ -31,6 +31,7 @@
 from jaxtyping import Array, Float
 from jaxutils import Dataset
 import jaxkern as jk
+import jax
 
 import gpjax as gpx